A couple comments here... First, make sure you have applied all bug fixes, as there were some fairly serious issues with running constant pH MD with multiple titratable residues. Second, you should expect larger fluctuations in constant pH simulations, since you're abruptly changing charges when protonation moves are accepted. Make sure you carefully heat and equilibrate your system with restraints before you begin to run production dynamics. One other comment: you should probably switch from the Berendsen thermostat (ntt=1) to the Langevin thermostat (ntt=3), and change tautp to gamma_ln (see the manual for more details). The thermostat has no effect on the state energies, so it won't affect sampled protonation states.